Revisiting Vibrational Spectroscopy to Tackle the Chemistry of Zr6O8 Metal-Organic Framework Nodes

The metal-organic framework MOF-808 contains Zr6O8 nodes with a high density of vacancy sites, which can incorporate carboxylate-containing functional groups to tune chemical reactivity. Although the postsynthetic methods to modify the chemistry of the Zr6O8 nodes in MOFs are well known, tackling these alterations from a structural perspective is still a challenge. We have combined infrared spectroscopy experiments and first-principles calculations to identify the presence of node vacancies accessible for chemical modifications within the MOF-808. We demonstrate the potential of our approach to assess the decoration of MOF-808 nodes with different catechol–benzoate ligands. Furthermore, we have applied advanced synchrotron characterization tools, such as pair distribution function analyses and X-ray absorption spectroscopy, to resolve the atomic structure of single metal sites incorporated into the catechol groups postsynthetically. Finally, we demonstrate the catalytic activity of these MOF-808 materials decorated with single copper sites for 1,3-dipolar cycloadditions.

The mixture was stirring during 15 minutes. Then, a metal salt (3 Eq, 44 µmol) was added.
The reaction mixture was stirred at room temperature for 1 hour in a sealed vial. The solid was centrifuged and washed three times with methanol yielding the corresponding metalated MOF as a powder. Metal salts used: FeCl 2 , NiBr 2 , CuBr, Mn(AcO) 2 , Hg(AcO) 2 , CoBr 2 . S-5

S2 Powder X-ray diffraction
Powder X-ray diffraction (PXRD) data were measured with a Bruker D8 diffractometer with a copper source operated at 1600 W, with step size = 0.02 • and exposure time = 0.5 s/step with a Bragg-Brentano geometry Samples were placed on a borosilicate sample holder. All the samples were grinded prior to analysis unless otherwise stated. Data were measured using a continuous 2θ scan from 3.0-45 • θ. Le Bail refinement was made to all powder samples using JANA2006 program. S1 Pseudo-Voigt peaks shapes were used along with a simple axial divergence correction. The lattice parameters, was refined against the values obtained from the CIF S2 in the 2θ range of 3-45 • . The zero-point error was also refined.

S3 Fourier-transform infrared spectroscopy
Attenuated total reflectance fourier-transform infrared spectroscopy (ATR-FTIR) spectra were recorded using FT-IR spectrometer Perkin Elmer model Spectrum 100, equipped with a diamond/ZnSe crystal. ATR-FTIR data was collected in the range of 500-4000 cm −1 with 32 scans per measure.

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Nitrogen adsorption and desorption isotherms were measured at 77 K using a Micromeritics ASAP 2020 system. The samples were outgassed at indicated temperature for 16 h before the measurements. The specific surface areas (BET) were calculated by application of the Brunauer-Emmett-Teller equation taking the area of the nitrogen molecule as 0.162 nm 2 . The linear range of the BET equation normally located between 0.05-0.35 P/P 0 , was much narrower and displaced to lower relative pressures for all materials studied due to their microporous natures taking the linear range: P/P 0 = 0.015-0.1. The micropore volume and external surface area, i.e. the area not associated with the micropores, were calculated using a t-plot analysis. taking the thickness of an adsorbed layer of nitrogen as 0.354 nm and assuming that the arrangement of nitrogen molecules in the film was hexagonal close packed.
The mesopore volumes of the materials were calculated from the volume of gas adsorbed at a relative pressure of 0.6 on the desorption branch of the isotherms, equivalent to the filling of all pores below 50 nm, minus the microporosity calculated from the corresponding t-plot.
The total pore volume was calculated from the volume of gas adsorbed at a relative pressure of 0.95 on the absorption branch of the isotherms.
Pore-size-distribution (PSD) curves were obtained from the adsorption branches using non-local density functional theory (NLDFT) method for a cylinder pore in pillared clays.     S-20

S5 Thermogravimetric analyses
Thermogravimetric analyses (TGA) were carried out on a TA Instruments Q500 thermobalance oven with a Pt sample holder and mass detector; N 2 was used as purge gas, at a flow rate of 90 mL/min; the samples were heated from 25 to 1000 • C at a rate of 10 • C/min Figure S26: TGA analysis of MOF-808-P (red) and differential curve (blue). Figure S27: TGA analysis of 23-DHBA-MOF-808 (red) and differential curve (blue).

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S8 X-ray pair distribution function analyses X-ray pair distribution function (PDF) analyses. Synchrotron X-ray total scattering data suitable for PDF analyses were collected at the P02.1 beamline S3 at PETRA IIII (Deutsches Elektronen-Synchrotron) at beamline P02.1 on beamtimes I-20190208-EC and I-20190239-EC. Samples were ground into a fine powder and loaded into kapton capillaries (0.7 mm i.d.) and sealed. Data were collected using a Perkin Elmer XRD1621 CN3 -EHS.
Empty capillary and background total scattering data were corrected for in data processing.
Samples were ground into borosilicate capillaries (1 mm i.d.) and flame-sealed. Data scans were collected during 10 minutes. Empty capillary and background total scattering data were corrected for in data processing. Sample data were processed to a Qmax of 22 Å −1 (λ = 0.1616 Å, 76 keV). Geometric corrections and reduction to 1D data used DAWN Science software. S4 Differential pair distribution function (dPDF) data were obtained by subtraction of a control PDF data of MOF-808 to that of the functionalized MOF-808 sample. These analyses were performed in real-space, after applying a normalisation factor to the total PDF data.
S-33 Signals that could not be easily interpreted or visualized were designated as multiplet (m).
Coupling constants (J) are indicated in Hz.
S-39 S10 Catalytic tests 1,3-dipolar cycloaddition. 5 mg of Cu-DHBA-MOF-808 were added to a stirred solution of benzyl azide ( 100 µL, 0.8 mmol, 1 eq) and the corresponding alkyne (0.91 mmol, 1.15 eq) in dry and deoxigenated EtOH (5 mL). The reaction mixture was heated at 70 • C for 16 h. Then the reaction was filtered thought a 0.22 µm nylon syringe filter, and 1,3,5trimethoxybenze (61 mg, 0.4 mol, 0.5 eq) was added to the reaction mixture. The solvent is removed in vacuo. The resulting solid is dissolved in ethyl acetate, and washed with water and brine. The organic layers are separated, dried and the solvent is removed in vacuo. The reaction yield is quantified by quantitative (qNMR) using 1,3,5-trimethoxybenze as internal standard.
Recyclability tests 5 mg of Cu-DHBA-MOF-808 were added to a stirred solution of benzyl(100 µL, 0.8 mmol, 1 eq) and phenylacetylene (0.91 mmol, 1.15 eq) in dry and deoxigenated EtOH. The reaction mixture was heated at 70 • C for 16 h. Then the reaction was filtered centrifuged and the MOF separated. 1,3,5-trimethoxybenze (61 mg, 0.4 mol, 0.5 eq) was added to the reaction mixture. The reaction yield is quantified by quantitative (qNMR) using 1,3,5-trimethoxybenze as internal standard. The MOF is washed with water and methylenchloride to remove any trace of salt, reagent, or product. The product is oven-dried at 50 • C overnight yields the clean catalytic material.
S-40 Figure S56: PXRD data of Cu-2,3-DHBA-MOF-808 before and after catalysis.   unit extracted from the crystal structure and coordinated by six BTC ligands. The distal carboxylate groups were protonated to avoid a spurious electron charge accumulation. The whole structure was placed on a cubic unit cell with a 33 Å edge in such a way that the distance between periodical imagines is minimised and leaving room enough to introduce the ligands of the functionalisation. This fragment, that we will discuss in depth in the next section, allows us to study the main structural and vibrational properties pristine MOF-808 and the subsequent functionalisation with 2,3-and 3,4-DHBA acid ligands.
All equilibrium geometries were obtained in our cluster models using a conjugate gradient algorithm in combination with electronic self-consistent loops. The self-consistent electronic S-43 loops were converged with a tolerance better than 10 −6 eV and the stopping criterion for the structural optimization was that forces upon atoms had to be smaller than 0.005 eV/Å. This strict criterion in forces is needed to ensure the success of the subsequent normal mode analysis, where a true energy minimum is required. Otherwise, spurious imaginary modes may appear. During the structural relaxations the oxygen and hydrogen atoms belonging to the distal carboxylate groups were fixed on their bulk positions to reproduce the real MOF environment while all the rest atoms were free to relax in order to find their equilibrium positions.
The vibrational properties of pristine and functionalized MOF-808 were investigated following a normal mode analysis under the classical harmonic approximation. This approach consists of the direct diagonalization of the mass-weighted Hessian matrix that appears when solving the atomic equations of motion using normal coordinates. S11,S12 The Hessian matrix is numerically obtained by means of finite differences considering a total of six displacements of ±0.02 Å per atom along the three Cartesian coordinates.
Once the normal modes (eigenvectors and eigenfrequencies) are known, the IR intensity of each mode is estimated as described in detail in previous work. S13 Essentially, the IR intensity of the nth normal mode, I IR n , is related to the square of the variation of the electric dipole moment along the vibration. S11 In turn, it depends on the so-called Born effective charges Z * αβ,τ as S14 where N is the number of atoms in our system and A τ β,n is the nth eigenvector. Notice that the Born effective charges can be directly calculated within DFT methods in the frame of the linear response theory using Density Functional Perturbation Theory (DFPT). S15,S16 After collecting the IR intensities of all individual modes, a complete IR spectrum for the system can be generated as a sum of continuous Lorentzian functions centered in each eigenfrequency.
A smearing of 3 cm −1 is considered for the Lorentzian functions because it is a balance S-44 between a good resolution and providing an appearance similar to the experimental spectra.
It is worth noting that the IR intensity obtained with Eq. (S1) is related to the absorbance (A) measurement. If we want to convert it to transmittance (T ), we have to take into account that T = 10 −A , as we have made for the present work. S-45

S12 Cluster models
We have studied the structural and vibrational properties of bare and functionalized MOF-808 following a cluster-type approach. As we pointed out in the previous section, due to the large size of the unit cell, it is impossible to calculate the vibrational modes of the whole crystal structure with periodic boundary conditions. The selected cluster model consists of Although not completely equivalent, all other possibilities will be closely related to one of these distributions.
The bonding of DHBA molecules takes place through the carboxylate groups acting as bidentante ligands, similarly to the original BTC linkers contained in the pristine crystal structure. We must say that for the 2,3-isomer is spatially possible a mixed carboxylate/phenolate coordination mode similar to the one found in MOF-74. However, our calcu-S-46 Moreover, the stability of the [Zr 6 O 8 H 4 ] 12+ polyhedra seems to be affected proceeding this way. Thus, we restrict our analysis to the 2,3-and 3,4-functionalization through the carboxylate groups, the only one predicted as stable by our calculations. Taking into account this circumstance, there are several ways for the incorporation of the ligands, but in all of them, the carboxylate ligands must bond to two adjacent Zr metal centers. This is because the coordination to the same metal center would lead to an unnatural (too small) COO bond angle, being an unfavourable choice. Since, we have a total of twelve outer coordination sites originally occupied by hydroxy/water ligands, all possible coordination modes reduce essentially to the three possibilities depicted in figure S60. By analogy to the benzene nomenclature with three substituents, we have labelled these coordination modes as 123, 124 and 135.
Our calculations do not show a clear preference for any of these coordination modes. It is true there are slight energy differences between them and with opposite trends for 2,3and 3,4-isomers. Namely, we find that the most stable configuration for the 2,3-isomer is 135 configuration, being the 124 and 123 slightly less energetically favourable by 0.27 eV and 0.49 eV respectively. Conversely, the 123 configuration is slightly more energetically favourable for the 3,4-isomer following the 123 > 124 > 135 trend. In this case the 124 and 135 configurations are 0.19 eV and 0.23 eV less stable than the most stable 123 configuration.
These small energy differences arise from the eventual formation of intra or interligand Hbonds, but all the configurations display basically the same features, as it can be observed in the figure and a similar energetics.
S-48 S13 Further IR theoretical spectra In figures S61 and S62 we show the theoretical IR spectra of functionalized MOF-808 in all the adsorption configurations that we have discussed in the previous section. All of them display basically the same IR features including the new signal at 1200 cm −1 arising from the new ligands. In the main text, we have included for comparison only the spectrum of the most energetically favourable configuration for each isomer. Figure S61: Theoretical IR spectra of MOF-808 functionalized with three 2,3-BHBA ligands in the equatorial plane. We show the IR spectra of the three configurations considered in this work. Figure S62: Theoretical IR spectra of MOF-808 functionalized with three 3,4-BHBA ligands in the equatorial plane. We show the IR spectra of the three configurations considered in this work. S-49